if (namefile != "") { nameMap = m->readNames(namefile); }
else if (countfile != "") {
CountTable ct;
- ct.readTable(countfile, false);
+ ct.readTable(countfile, false, false);
nameMap = ct.getNameMap();
}
bool done = false;
int count = 0;
-
+
+
while (!done) {
if (m->control_pressed) { in.close(); outSummary.close(); return 1; }
ambigBases.push_back(current.getAmbigBases());
longHomoPolymer.push_back(current.getLongHomoPolymer());
}
-
count++;
outSummary << current.getName() << '\t';
outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';